Allegations against diocesan priests, members of religious orders and missionary societies will all be included in the audit.
It will seek to determine the numbers of allegations in each diocese and whether the complaints were properly handled by church authorities.
The bishops have given a commitment that any allegations uncovered that were not properly handled will be referred to the gardaí or the PSNI, and to relevant health authorities north and south.
The audit will concentrate on complaints involving alleged perpetrators still alive rather than older cases.
Ian Elliot, chief executive of the National Board for the Safeguarding of Children in the Catholic Church, said this was a matter of prioritising current and future risks to children.
"What we are trying to do is confirm the safety and wellbeing of children in the church today and going forward. There are resource issues. We are trying to put the emphasis where it needs to be, and current risk is what concerns people."
He added that the Government inquiries into child sex abuse in the dioceses of Ferns, Dublin and Cloyne, had already placed in the public domain the very bad practices that existed in relation to child protection in the Catholic Church.
The audit will be carried out by the board, but Mr Elliot said their work would be reviewed by experts from outside of the church.
He expected it would take two to two and a half years to complete the audit.
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